The objective was to study changes in water-saturated biodiesel irradiated by electron beam and to analyse them considering the influence of absorbed dose. Based on obtained results it can be concluded that irradiation did not affect ester groups in FAME molecules, but strongly influenced on double bonds. Total ester content decreased linearly with the increase in absorbed dose, causing FAME not to meet the requirement of PN-EN 14214 concerning the ester content (96.5 wt%). Therefore, the use of ionizing radiation to improve biodiesel properties is unlikely, but it is worth to consider electron beam sterilisation of this biofuel.